Course content
These materials were part of the past ‘PerMedCoE summer school: from pathway modelling tools to cell-level simulations‘ course, which took place in June 2023. Please refer to the course pages to check details about the live event and the original programme.
The contents table below outlines the different sessions that were included in the course, as well as the format of the materials (slides/practicals) and each session’s trainer. Either proceed through the materials using the arrows at the end of each page or pick your topic of interest from the table below to skip straight to it.
Presentation slides – View or download the slides
Practicals – View or download the slides, exercises, datasets, analysis scripts and results
| Format | Subject | Trainer |
| Working with High Performance Computing (HPC) – Introduction to HPC – Containers, building blocks and workflows | Javier Conejero and Henrik Nortamo |
| Logical modelling of cell signalling | Pablo Rodríguez Mier and Denes Turei |
| Constraint-Based Reconstruction and Analysis for metabolic modelling | Miguel Ponce de León and Miroslav Kratochvil |
| Qualitative modelling of biological systems with MaBoSS | Vincent Noël and Marco Ruscone |
| Simulation of multicellular systems | Arnau Montagud, Marco Ruscone, Miguel Ponce de León and Thalia Diniaco |
| Keynote lectures | ||
| Next generation molecular tumor boards: systems biology and functional precision medicine | Åsmund Flobak |
| Bias in research | Davide Cirillo |